Mutagenetix > Incidental Mutation

Incidental Mutation 'R1630:Lhx6'

254722

Institutional Source

Beutler Lab

Gene Symbol

Lhx6

Ensembl Gene

ENSMUSG00000026890

Gene Name

LIM homeobox protein 6

Synonyms

MMRRC Submission

039667-MU

Accession Numbers

Essential gene?

Probably essential (E-score: 0.930) question?

Stock #

R1630 (G1)

Quality Score

Status

Validated

Chromosome

Chromosomal Location

35971965-35995420 bp(-) (GRCm39)

Type of Mutation

missense

DNA Base Change (assembly)

A to G at 35992913 bp (GRCm39)

Zygosity

Heterozygous

Amino Acid Change

Tyrosine to Histidine at position 140 (Y140H)

Ref Sequence

ENSEMBL: ENSMUSP00000108584 (fasta)

Gene Model

predicted gene model for transcript(s): [ENSMUST00000112960] [ENSMUST00000112961] [ENSMUST00000112963] [ENSMUST00000112966] [ENSMUST00000112967] [ENSMUST00000148852]

AlphaFold

Q9R1R0

Predicted Effect

probably damaging
Transcript: ENSMUST00000112960
AA Change: Y140H

PolyPhen 2 Score 0.997 (Sensitivity: 0.41; Specificity: 0.98)

SMART Domains

Protein: ENSMUSP00000108584
Gene: ENSMUSG00000026890
AA Change: Y140H

Domain	Start	End	E-Value	Type
low complexity region	71	94	N/A	INTRINSIC
LIM	98	151	7.34e-13	SMART
LIM	159	213	3.17e-17	SMART
HOX	248	310	1.1e-23	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000112961
AA Change: Y111H

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000108585
Gene: ENSMUSG00000026890
AA Change: Y111H

Domain	Start	End	E-Value	Type
low complexity region	42	65	N/A	INTRINSIC
LIM	69	122	7.34e-13	SMART
LIM	130	184	3.17e-17	SMART
HOX	219	281	1.1e-23	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000112963
AA Change: Y111H

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000108587
Gene: ENSMUSG00000026890
AA Change: Y111H

Domain	Start	End	E-Value	Type
low complexity region	42	65	N/A	INTRINSIC
LIM	69	122	7.34e-13	SMART
LIM	130	184	3.17e-17	SMART
HOX	219	281	1.1e-23	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000112966
AA Change: Y111H

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000108590
Gene: ENSMUSG00000026890
AA Change: Y111H

Domain	Start	End	E-Value	Type
low complexity region	42	65	N/A	INTRINSIC
LIM	69	122	7.34e-13	SMART
LIM	130	184	3.17e-17	SMART
HOX	219	281	1.1e-23	SMART

Predicted Effect

probably damaging
Transcript: ENSMUST00000112967
AA Change: Y140H

PolyPhen 2 Score 0.991 (Sensitivity: 0.71; Specificity: 0.97)

SMART Domains

Protein: ENSMUSP00000108591
Gene: ENSMUSG00000026890
AA Change: Y140H

Domain	Start	End	E-Value	Type
low complexity region	71	94	N/A	INTRINSIC
LIM	98	151	7.34e-13	SMART
LIM	159	213	3.17e-17	SMART
HOX	248	310	1.1e-23	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000137436

Predicted Effect

probably damaging
Transcript: ENSMUST00000148852
AA Change: Y111H

PolyPhen 2 Score 0.980 (Sensitivity: 0.75; Specificity: 0.96)

SMART Domains

Protein: ENSMUSP00000135693
Gene: ENSMUSG00000026890
AA Change: Y111H

Domain	Start	End	E-Value	Type
low complexity region	42	65	N/A	INTRINSIC
LIM	69	122	7.34e-13	SMART
LIM	130	184	3.17e-17	SMART
HOX	219	281	1.1e-23	SMART

Predicted Effect

noncoding transcript
Transcript: ENSMUST00000187180

Meta Mutation Damage Score

0.9213

Coding Region Coverage

1x: 99.0%
3x: 98.1%
10x: 95.6%
20x: 90.1%

Validation Efficiency

100% (67/67)

MGI Phenotype

FUNCTION: [Summary is not available for the mouse gene. This summary is for the human ortholog.] This gene encodes a member of a large protein family that contains the LIM domain, a unique cysteine-rich zinc-binding domain. The encoded protein has tandem LIM domains as well as a DNA-binding homeodomain. The protein functions as a transcription factor involved in embryogenesis and head development and is highly expressed in neural crest derived mesenchyme cells. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jan 2017]
PHENOTYPE: Homozygous mutation of this gene results in impaired migration and specification of cortical interneurons, postnatal lethality and weakness. [provided by MGI curators]

Allele List at MGI

Other mutations in this stock

Total: 60 list
Gene	Ref	Var	Chr/Loc	Mutation	Predicted Effect	Zygosity
4931429P17Rik	C	A	13: 48,114,201 (GRCm39)		noncoding transcript	Het
9930012K11Rik	T	C	14: 70,394,629 (GRCm39)	E175G	probably benign	Het
A630091E08Rik	A	G	7: 98,192,814 (GRCm39)		noncoding transcript	Het
Atm	A	T	9: 53,390,973 (GRCm39)	L1867Q	probably damaging	Het
Atp5f1a	A	G	18: 77,865,267 (GRCm39)	D63G	possibly damaging	Het
Baz2b	A	T	2: 59,836,474 (GRCm39)	S20T	unknown	Het
C1qtnf7	G	A	5: 43,766,503 (GRCm39)	C34Y	possibly damaging	Het
Cactin	A	G	10: 81,159,559 (GRCm39)	T353A	probably benign	Het
Cdyl	A	G	13: 35,867,786 (GRCm39)	K21E	possibly damaging	Het
Crispld1	A	G	1: 17,799,022 (GRCm39)	T48A	probably benign	Het
Csmd3	T	A	15: 47,701,918 (GRCm39)	T1722S	possibly damaging	Het
Dapk1	A	T	13: 60,877,345 (GRCm39)	E528V	probably damaging	Het
Dennd4a	A	G	9: 64,779,164 (GRCm39)	D549G	probably benign	Het
Dnajc5b	C	A	3: 19,628,905 (GRCm39)	N66K	probably damaging	Het
Dusp16	G	T	6: 134,697,524 (GRCm39)	R250S	probably damaging	Het
F10	A	G	8: 13,105,551 (GRCm39)	N384S	probably benign	Het
Gabrr2	A	G	4: 33,085,647 (GRCm39)	S331G	probably damaging	Het
Gm12185	A	C	11: 48,798,717 (GRCm39)	I592S	probably benign	Het
Gm9755	T	C	8: 67,967,312 (GRCm39)		noncoding transcript	Het
Hspg2	T	C	4: 137,245,746 (GRCm39)	L913P	probably damaging	Het
Ifna1	T	A	4: 88,768,566 (GRCm39)	S81R	probably benign	Het
Iqgap2	T	C	13: 95,826,293 (GRCm39)	K510E	probably benign	Het
Kirrel1	C	T	3: 86,996,458 (GRCm39)	M380I	probably null	Het
Lix1	A	G	17: 17,677,420 (GRCm39)	H205R	probably damaging	Het
Masp2	A	T	4: 148,698,490 (GRCm39)	T524S	probably benign	Het
Mndal	A	C	1: 173,701,958 (GRCm39)	F115V	possibly damaging	Het
Morc3	C	A	16: 93,663,421 (GRCm39)	N541K	probably benign	Het
Mslnl	G	A	17: 25,961,908 (GRCm39)	V128M	probably damaging	Het
Myocd	A	G	11: 65,087,220 (GRCm39)	S236P	probably benign	Het
Nes	T	A	3: 87,884,984 (GRCm39)	V1037E	probably benign	Het
Nfkbil1	A	G	17: 35,440,140 (GRCm39)	W178R	probably damaging	Het
Nobox	A	T	6: 43,284,146 (GRCm39)	C8*	probably null	Het
Nwd1	A	G	8: 73,393,657 (GRCm39)	T348A	possibly damaging	Het
Or1e23	T	C	11: 73,407,546 (GRCm39)	T160A	probably damaging	Het
Or5bw2	T	C	7: 6,573,673 (GRCm39)	S228P	probably damaging	Het
Or8k17	A	G	2: 86,066,430 (GRCm39)	S243P	probably damaging	Het
Osbp2	T	C	11: 3,667,167 (GRCm39)	T448A	probably benign	Het
Plrg1	A	G	3: 82,966,070 (GRCm39)	D75G	probably benign	Het
Ppp1r8	T	C	4: 132,556,748 (GRCm39)	E213G	probably benign	Het
Rad54l2	A	G	9: 106,580,828 (GRCm39)	F898L	possibly damaging	Het
Rapgef6	TG	TGG	11: 54,437,223 (GRCm39)		probably null	Het
Rasl10a	G	C	11: 5,009,542 (GRCm39)	R110P	probably damaging	Het
Rttn	T	C	18: 89,061,078 (GRCm39)	I1082T	probably benign	Het
Sema6d	A	G	2: 124,506,265 (GRCm39)	D734G	possibly damaging	Het
Sgce	C	T	6: 4,719,476 (GRCm39)	V44M	probably damaging	Het
Sgo2b	A	G	8: 64,380,831 (GRCm39)	V667A	possibly damaging	Het
Shcbp1	A	T	8: 4,798,763 (GRCm39)	C118*	probably null	Het
Slain2	C	T	5: 73,133,347 (GRCm39)	P563S	probably damaging	Het
Slco1b2	A	T	6: 141,602,547 (GRCm39)	I167F	probably damaging	Het
Speg	T	C	1: 75,399,621 (GRCm39)	L2356P	probably damaging	Het
Sptbn4	A	G	7: 27,118,164 (GRCm39)	V305A	probably benign	Het
Sspo	G	A	6: 48,434,658 (GRCm39)	R1050H	probably benign	Het
Tmem106b	A	G	6: 13,081,540 (GRCm39)	N149S	probably benign	Het
Tmem200a	T	C	10: 25,868,812 (GRCm39)	T486A	probably damaging	Het
Tmem212	T	A	3: 27,939,250 (GRCm39)	T79S	possibly damaging	Het
Ttll11	A	G	2: 35,779,337 (GRCm39)	V471A	probably damaging	Het
Vill	A	G	9: 118,899,769 (GRCm39)	N318D	probably benign	Het
Vmn2r102	A	G	17: 19,899,032 (GRCm39)	D458G	possibly damaging	Het
Zfp472	T	A	17: 33,196,952 (GRCm39)	C342*	probably null	Het
Zfp963	A	T	8: 70,196,837 (GRCm39)		probably benign	Het

Other mutations in Lhx6

Allele	Source	Chr	Coord	Type	Predicted Effect	PPH Score
IGL00088:Lhx6	APN	2	35,981,728 (GRCm39)	splice site	probably benign
IGL01391:Lhx6	APN	2	35,993,477 (GRCm39)	missense	probably benign	0.00
IGL01413:Lhx6	APN	2	35,993,528 (GRCm39)	missense	probably benign	0.24
IGL03154:Lhx6	APN	2	35,984,455 (GRCm39)	splice site	probably null
R1546:Lhx6	UTSW	2	35,981,049 (GRCm39)	missense	probably benign	0.00
R1785:Lhx6	UTSW	2	35,977,470 (GRCm39)	nonsense	probably null
R1786:Lhx6	UTSW	2	35,977,470 (GRCm39)	nonsense	probably null
R1792:Lhx6	UTSW	2	35,977,387 (GRCm39)	missense	probably damaging	1.00
R2126:Lhx6	UTSW	2	35,981,336 (GRCm39)	missense	possibly damaging	0.94
R2145:Lhx6	UTSW	2	35,977,478 (GRCm39)	missense	probably benign	0.01
R2167:Lhx6	UTSW	2	35,993,371 (GRCm39)	missense	probably damaging	1.00
R2393:Lhx6	UTSW	2	35,981,402 (GRCm39)	missense	probably benign	0.22
R5102:Lhx6	UTSW	2	35,984,222 (GRCm39)	splice site	probably null
R5418:Lhx6	UTSW	2	35,977,378 (GRCm39)	critical splice donor site	probably null
R6735:Lhx6	UTSW	2	35,981,390 (GRCm39)	missense	probably damaging	0.99
R7462:Lhx6	UTSW	2	35,974,083 (GRCm39)	missense	possibly damaging	0.86
R7546:Lhx6	UTSW	2	35,993,357 (GRCm39)	critical splice donor site	probably null
R8870:Lhx6	UTSW	2	35,995,232 (GRCm39)	unclassified	probably benign
R9192:Lhx6	UTSW	2	35,981,145 (GRCm39)	missense	probably benign	0.10
R9667:Lhx6	UTSW	2	35,980,979 (GRCm39)	missense	possibly damaging	0.93

Predicted Primers

PCR Primer
(F):5'- CTCCCTTCTGTGTAAGACGTGCTG -3'
(R):5'- GTTCCAACAAGAGAATGCAAGGCTG -3'

Sequencing Primer
(F):5'- CTGTGTAAGACGTGCTGAGTAG -3'
(R):5'- CCTTGAGCCTCTCTGTATTATAGAAG -3'

Posted On

2014-12-23